whichever one suits your needs (and depending on the instrument you have or budget for an instrument)

i will say that affymetrix microarrays and agilent microarrays (not just expression) fill a similar niche.

i'm not familiar with illumina expression beadchips (we have an illumina instrument in another lab but they are using it for immunoassays (i think)).

-mdfenko-

Which one is better a Honda or Toyota? A lot of it is personal preference.

If you are studying an organism such as human or mouse that is on all three platforms, then you really are okay with any of them (depending on application - are you talking gene expression, SNPs, methylation?). One might be more cost effective than the other. Also they are sold in different formats. Depending on your service provider - you may have to provide groups of 12 samples to use Illumina arrays, groups of 4 or 8 to use Agilent arrays but any number of Affy arrays will work. However, the Illumina arrays might be cheaper per sample.

Talk to your service provider. We support all three platforms and they all provide excellent data as long as the experiment was well designed.

-Winegarden-

agilent arrays come in one, two, four and eight samples per slide. you are not limited to four or eight.

(and i drive a subaru)

-mdfenko-

Sorry I'm showing my human/mouse centric research bias. For expression those arrays tend to be 4/8 up. But yes you are correct there are Agilent arrays in 1-up and 2-up format of course. Similarly Illumina come in 4, 6 and 12 up depending on application.

-Winegarden-

However, I heard Agilent is not dedicated or good for SNPs... not sure how true it is...

-Adrian K-

However, I heard Agilent is not dedicated or good for SNPs... not sure how true it is...

agilent offers hybrid cgh-snp microarrays with ~60k or ~120k snps (depending on configuration). i haven't used them so i can't say that they are any good but if they are of similar quality and usefulness to agilents other microarrays then they should work well.